Predicting Pathogenicity of CDH1 Gene Variants in Patients with Early-onset Diffuse Gastric Cancer from Western Mexico

Autor:	Josefina Yoaly Sánchez-López, Héctor Rangel-Villalobos, Lourdes Del Carmen Rizo-de la Torre, Andrea Virginia Ruiz-Ramírez, Andrea M. García-Muro, Ernesto Prado-Montes-de-Oca, María Teresa Magaña-Torres, José Alonso Aguilar-Velázquez, Azaria García-Ruvalcaba
Rok vydání:	2021
Předmět:	Sanger sequencing biology Single-nucleotide polymorphism Promoter General Medicine Molecular biology Linea CDH1 symbols.namesake Exon Germline mutation symbols biology.protein Gene
Zdroj:	Revista de investigaci�n Cl�nica. 73
ISSN:	0034-8376 3456-1447
DOI:	10.24875/ric.20000470
Popis:	espanolAntecedentes: el cancer gastrico difuso de inicio temprano (EODGC) se presenta a los 50 anos de edad o antes. Las mutaciones patogenicas y las deleciones de la linea germinal en el gen CDH1 (E-cadherina) son factores geneticos bien documentados asociados con las causas de EODGC. Objetivo: El objetivo del estudio fue estudiar las variantes de la linea germinal de CDH1 y su potencial impacto funcional en pacientes con EODGC en una poblacion mexicana. Metodos: Estudiamos a siete pacientes con EODGC de un centro de investigacion biomedica en el occidente de Mexico. Las variantes se identificaron mediante secuenciacion de Sanger y amplificacion de sonda dependiente de ligadura multiple. El software DeepSEA y SNPClinic v.1.0 y las bases de datos Ensembl (1000 Genomes Project, 1kGP) y ClinVar se utilizaron para predecir polimorfismos funcionales de un solo nucleotido (SNP). La mezcla genetica de los pacientes mexicanos fue corroborada por el genotipado y analisis de estructura de 22 loci de repeticion en tandem cortos. Resultados: Encontramos 12 variantes de CDH1 de la linea germinal en todos los pacientes con EODGC, y todas se consideran polimorfismos: rs34561447, rs5030625, rs16260, rs1330727101, rs28372783, rs942269593, rs3743674, rs1801552, rs65910rs2691717 La prediccion de los SNP reguladores en el promotor sugiere un papel para un retrovirus en EODGC que induce la transcripcion de genes relacionados con el interferon a traves de la senalizacion del factor 3 de respuesta al interferon del receptor tipo toll, ya que tres SNP en el promotor CDH1 alteran tres sitios de union para esto. Ademas, los SNP rs28372783 y rs1801026 podrian alterar la activacion de linfocitos dependiente de telomerasa mediada por factores estimulantes 1 (USF1) / USF2 en EODGC. Otro resultado interesante es un cortocircuito dependiente de CTCF Isoforma CDH1 que carece del exon 14, probablemente debido a la omision del exon mediada por rs33964119. Conclusiones: No se encontraron mutaciones patogenas clasicas de la linea germinal en el gen CDH1 en estos 7 pacientes con EODGC. Sin embargo, los enfoques in silico revelaron la posible participacion de un retrovirus y una isoforma de cadherina E mas corta en EODGC. No obstante, se necesitan mas ensayos in vitro e in vivo para confirmar estas predicciones. (REV INVEST CLIN. 2021; 73 (3): XX-XX) EnglishBackground: Early-onset diffuse gastric cancer (EODGC) occurs at or before 50 years of age. Pathogenic mutations and germline deletions in the CDH1 gene (E-cadherin) are well-documented genetic factors associated with the causes of EODGC. Objective: The objective of the study was to study CDH1 germline variants and their potential functional impact in patients with EODGC in a Mexican population. Methods: We studied seven EODGC patients from a biomedical research center in western Mexico. Variants were identified by Sanger sequencing and multiplex ligation-dependent probe amplification. The DeepSEA and SNPClinic v.1.0 software and the Ensembl (1000 Genomes Project, 1kGP) and ClinVar databases were used to predict functional single-nucleotide polymorphisms (SNPs). The genetic admixture of the Mexican patients was corroborated by 22 short tandem repeat loci genotyping and structure analysis. Results: We found 12 germline CDH1 variants in all EODGC patients, and all of them are considered as polymorphisms: rs34561447, rs5030625, rs16260, rs1330727101, rs28372783, rs942269593, rs3743674, rs1801552, rs34939176, rs33964119, rs3556654, and rs1801026. The prediction of regulatory SNPs in the promoter suggests a role for a retrovirus in EODGC that induces the transcription of interferon-related genes through toll-like receptor-interferon response factor 3 signaling, as three SNPs in the CDH1 promoter alter three binding sites for this transcription factor. In addition, SNPs rs28372783 and rs1801026 could alter upstream stimulatory factors 1 (USF1)/USF2-mediated telomerase-dependent lymphocyte activation in EODGC. Other interesting result is a CTCF-dependent shorter CDH1 isoform lacking exon 14, probably due to exon-skipping mediated by rs33964119. Conclusions: Classical pathogenic germline mutations in the CDH1 gene were not found in these 7 EODGC patients. However, the in silico approaches revealed the possible involvement of a retrovirus and a shorter E-cadherin isoform in EODGC. Nevertheless, further in vitro and in vivo assays are needed to confirm these predictions. (REV INVEST CLIN. 2021;73(3):XX-XX)
Databáze:	OpenAIRE
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